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Macadamia integrifolia is a representative of the large basal eudicot family Proteaceae and the main progenitor species of the Australian native nut crop macadamia. Since its commercialisation in Hawaii fewer than 100 years ago, global production has expanded rapidly. However, genomic resources are limited in comparison to other horticultural crops...
Similar publications
Abnormal vertical growth (AVG) syndrome is a serious threat to the Australian macadamia industry as it decreases the yield of nuts by as much as 70% per annum. A lack of information on the cause of AVG has hindered the development of an effective disease management strategy. Discovery of genetic markers associated with disease resistance can be use...
Citations
... In A. thaliana, for example, AtPHT1;1 and AtPHT1;2 have approximately 98% nucleotide sequence identity (Mudge et al. 2002). The actual number of HpPHT1 genes may be closer to the 14 and 15 PHT1 sequences found in the genome assemblies of the Proteaceae M. integrifolia and T. speciosissima, respectively (Chen et al. 2022;Nock et al. 2020). ...
Background and aims
Phosphorus (P) is an essential plant nutrient and integral for crop yield. However, plants adapted to P-impoverished environments, such as Hakea prostrata (Proteaceae), are often sensitive to P supplies that would be beneficial to other plants. The strategies for phosphate uptake and transport in P-sensitive species have received little attention.
Methods
Using a recently-assembled transcriptome of H. prostrata, we identified 10 putative members of the PHOSPHATE TRANSPORTER1 (PHT1) gene family, which is responsible for inorganic phosphate (Pi) uptake and transport in plants. We examined plant growth, organ P concentrations and the transcript levels for the eight PHT1 members that were expressed in roots of H. prostrata at Pi supplies ranging from P-impoverished to P-excess.
Key results
Hakea prostrata plants suppressed cluster root growth above ecologically-relevant Pi supplies, whilst non-cluster root mass ratios were constant. Root P concentrations increased with increasing Pi supply. Of the eight H. prostrata PHT1 genes tested, four had relatively high transcript amounts in young roots suggesting important roles in Pi uptake; however, a maximum five-fold difference in expression between P-impoverished and P-excess conditions indicated a low P-responsiveness for these genes. The HpPHT1;8 and HpPHT1;9 genes were paralogous to Pi-responsive Arabidopsis thaliana PHT1;8 and PHT1;9 orthologues involved in root-to-shoot translocation of P, but only HpPHT1;9 was P responsive.
Conclusions
An attenuated ability of H. prostrata to regulate PHT1 expression in response to Pi supply is likely responsible for its low capacity to control P uptake and contributes to its high P sensitivity.
... Whole genome re-sequencing is a powerful NGS tool for characterizing genetic variation (Bentley 2006), and has been applied to study a variety of fruit and nut trees, including plum (Wei et al. 2021), peach (Yu et al. 2018), date palm (Hazzouri et al. 2015), sweet cherry (Xanthopoulou et al. 2020), and hazelnut (Cheng et al. 2019). In the case of macadamia, four chromosome-scale reference genomes have been reported to data (Lin et al. 2022;Niu et al. 2022;Nock et al. 2020;Xia et al. 2022), contributing to the research and genetic improvement of this tree crop. These available genomic resources enable the detection of genetic variation across macadamia accessions collected. ...
Macadamia (Macadamia integrifolia, and M. tetraphylla) production has increased rapidly in China over the past two decades. However, our understanding of the genetic diversity and genomic background of available macadamia germplasm resources remains limited. Here, we conducted whole genome resequencing of 208 macadamia accessions in a macadamia germplasm from China. In all, 1,110.83 Gb of clean reads and 458,205,696 single nucleotide polymorphisms (SNPs) were identified, including 5,470,885 high-quality SNPs. The overall genetic diversity of 208 macadamia accessions showed nucleotide diversity (Pi), expected heterozygosity (He), and observed heterozygosity (Ho) values of 1.716 × 10–3, 0.270, and 0.202, respectively. Australian germplasm generally possessed the highest genetic diversity, followed by Chinese germplasm, with macadamia germplasm resources introduced from the United States exhibiting the lowest genetic diversity. Furthermore, both phylogenetic and PCA analyses consistently clustered American accessions together. Genetic structure analysis divided the 208 accessions into nine groups, with moderate to high genetic differentiation found between different groups. These findings and genomic resources obtained from this study will be crucial for the strategic utilization of macadamia germplasm and will significantly contribute to future genome-wide associate studies.
... For instance, compared with Guire No.1, the plant height of H2 was higher, the diameter of the underground part of HAES695 was thicker, the taproot of A16, O.C and OV was longer, and the fresh weight of H2 was larger [19]. The HAES741 [20] genome analysis provides a good basis for yield component traits in macadamia [21]. Our previous studies showed that 12 months after grafting, the survey found that the survival rate of grafting with different rootstock combinations was between 75.33%~84.67%. ...
Macadamia nut plantings in China are expanding year by year. In order to further promote the superior varieties, this study analyzed the effects of different varieties of rootstock and scion on the survival rate as well as the effects of 18 different ratios of substrate composition on seedling growth were analyzed. The results showed that: The survival rate of HAES788 varieties as rootstock and Guire No.1 as scion was the highest, reaching 96%. The optimal grafting time in December was better than that in March. Substrate formulations 12, 13, 15 and 16 had agglomerated soil and well-developed root systems compared to the controls. Plant height, stem diameter, leaf length, leaf width, and dry weight of aboveground and underground parts were significantly higher than those of the control. In addition, the substrate formulations 12, 13, 15 and 16 significantly improved the organic matter, total nitrogen, and total potassium content of the substrate soils, but little on total phosphorus content. All in all, macadamia grafting times are best in December, with HAES788 and Guire No.1 being the best rootstock and scion. Substrate formulations 12, 13, 15 and 16 are the optimal formula. This study provides a solid foundation to produce high-quality macadamia seedlings.
... Recently, there has been increased interest in developing genomic resources for this crop (e.g. genome -Nock et al., 2020) due to its importance as a high-value, nutrient-dense food (Rengel et al., 2015;Navarro et al., 2016) that has undergone relatively little commercial breeding. In Hawaiʻi alone, there has been an increase in resources dedicated to the crop due to its large land uses (17,100 acres in 2019) and high value ($42 million USD) [6]. ...
Macadamia tetraphylla is a wild relative of the economically valuable crop Macadamia integrifolia. Genomic knowledge of crop wild relatives is central to determining their possible role in breeding programs to mitigate biotic and abiotic stress in the future. The goal of this project was to develop a genomic resource for macadamia agriculture in Hawaiʻi through constructing a transcriptome of M. tetraphylla and testing for hybridity in University of Hawaiʻi at Mānoa breeding material. The transcriptome assembly of M. tetraphylla revealed large differences in gene expression attributable to tissue type. Advanced breeding lines (HI862 and HI879) appear to be hybridized with the crop wild relative M. tetraphylla. Additionally, a putative M. tetraphylla tree sampled from a remnant orchard planting at the Waimānalo research station on Oahu did not match anecdotal accounts of the orchard as it appeared to be of hybrid ancestry.
... M. integrifolia is a dicotyledon plant with a genome (2n = 28) size of about 652-896 Mb [38]. At present, the genome sizes of two cultivars are known: 745 Mb for HEAS 741 [39] and 794 Mb for HEAS 344 (Kau) [40]. The domestication history of Macadamia is short, the record is clear, and the release of genome data provides the possibility of improving the efficiency of Macadamia breeding [40]. ...
Edible Macadamia is one of the most important commercial nut trees cultivated in many countries, but its large tree size and long juvenile period pose barriers to commercial cultivation. The short domestication period and well-annotated genome of Macadamia integrifolia create great opportunities to breed commercial varieties with superior traits. Recent studies have shown that members of the phosphatidylethanolamine binding protein (PEBP) family play pivotal roles in regulating plant architecture and flowering time in various plants. In this study, thirteen members of MiPEBP were identified in the genome of M. integrifolia, and they are highly similarity in both motif and gene structure. A phylogenetic analysis divided the MiPEBP genes into three subfamilies: MFT-like, FT-like and TFL1-like. We subsequently identified two TERMINAL FLOWER 1 homologues from the TFL1-like subfamily, MiTFL1 and MiTFL1-like, both of which were highly expressed in stems and vegetative shoots, while MiTFL1-like was highly expressed in young leaves and early flowers. A subcellular location analysis revealed that both MiTFL1 and MiTFL1-like are localized in the cytoplasm and nucleus. The ectopic expression of MiTFL1 can rescue the early-flowering and terminal-flower phenotypes in the tfl1-14 mutant of Arabidopsis thaliana, and it indicates the conserved functions in controlling the inflorescence architecture and flowering time. This study will provide insight into the isolation of PEBP family members and the key targets for breeding M. integrifolia with improved traits in plant architecture and flowering time.
... The genome sequences and corresponding annotations of four species with apparent fusion of multiple CHS gene copies were selected for manual inspection: Musa balbisiana [12], Musa troglodytarum [13], Macadamia integrifolia [14], and Nymphaea colorata [15]. All available paired-end RNA-seq data sets of these species were retrieved from the Sequence Read Archive via fastqdump [16] (Additional File 1 in [17]). ...
... We investigated the assembly and annotation process underlying the annotations of the four analyzed species. The Macadamia integrifolia assembly was produced with MaSuRCA v3.2.6 and ALLMAPS v.Jul-2019 [14,26,27]. The Musa balbisiana and Musa troglodytarum genome sequences were assembled with wtdbg v1.2.8 and Next-Denovo v2.4.0, respectively [12,13,28,29]. ...
Objective
Chalcone synthase (CHS) catalyzes the initial step of the flavonoid biosynthesis. The CHS encoding gene is well studied in numerous plant species. Rapidly growing sequence databases contain hundreds of CHS entries that are the result of automatic annotation. In this study, we evaluated apparent multiplication of CHS domains in CHS gene models of four plant species.
Main findings
CHS genes with an apparent triplication of the CHS domain encoding part were discovered through database searches. Such genes were found in Macadamia integrifolia, Musa balbisiana, Musa troglodytarum, and Nymphaea colorata. A manual inspection of the CHS gene models in these four species with massive RNA-seq data suggests that these gene models are the result of artificial fusions in the annotation process. While there are hundreds of seemingly correct CHS records in the databases, it is not clear why these annotation artifacts appeared.
... The genome sequences and corresponding annotations of four species with apparent fusion of multiple CHS gene copies were selected for manual inspection: Musa balbisiana [13], Musa troglodytarum [14], Macadamia integrifolia [15], and Nymphaea colorata [16]. All available paired-end RNA-seq data sets of these species were retrieved from the Sequence Read Archive via fastq-dump [17] (Additional File 1). ...
... We investigated the assembly and annotation process underlying the annotations of the four analyzed species. The Macadamia integrifolia assembly was produced with MaSuRCA v3.2.6 and ALLMAPS v.Jul-2019 [15,27,28]. The Musa balbisiana and M. troglodytarum genome sequences were assembled with wtdbg v1.2.8 and NextDenovo v2.4.0, respectively [13,14,29,30]. ...
Objective: Chalcone synthase (CHS) catalyzes the initial step of the flavonoid biosynthesis. The CHS encoding gene is well studied in numerous plant species. Rapidly growing sequence databases contain hundreds of CHS entries that are the result of automatic annotation. In this study, we evaluated apparent multiplication of CHS domains in CHS gene models of four plant species.
Main findings: CHS genes with an apparent triplication of the CHS domain encoding part were discovered through database searches. Such genes were found in Macadamia integrifolia, Musa balbisiana, Musa troglodytarum, and Nymphaea colorata. A manual inspection of the CHS gene models in these four species with massive RNA-seq data suggests that these gene models are the result of artificial fusions in the annotation process. While there are hundreds of apparently correct CHS records in the databases, it is not clear why these annotation artifacts appeared.
... Nelumbo nucifera (2n = 16) is a member of the family Nelumbonaceae from order Proteales, which was first sequenced in 2013 (Ming et al., 2013) and has further been updated in assembly (Gui et al., 2018;. Macadamia integrifolia (2n = 28) is a representative species of Proteales and its genome has been sequenced (Nock et al., 2020). Ranunculales is the earliest group diverging from other eudicots, including the genomes of Aquilegia coerulea (2n = 14) (Aköz and Nordborg, 2019), Aquilegia oxysepala var. ...
Eudicots account for ~75% of living angiosperms, containing important food and energy crops. Recently, high-quality genome sequences of several eudicots including Aquilegia coerulea and Nelumbo nucifera have become available, providing an opportunity to investigate the early evolutionary characteristics of eudicots. We performed genomic hierarchical and event-related alignments to infer homology within and between representative species of eudicots. The results provide strong evidence for multiple independent polyploidization events during the early diversification of eudicots, three of which are likely to be allopolyploids: The core eudicot-common hexaploidy (ECH), Nelumbo-specific tetraploidy (NST), and Ranunculales-common tetraploidy (RCT). Using different genomes as references, we constructed genomic alignment to list the orthologous and paralogous genes produced by polyploidization and speciation. This could provide a fundamental framework for studying other eudicot genomes and gene(s) evolution. Further, we revealed significantly divergent evolutionary rates among these species. By performing evolutionary rate correction, we dated RCT to be ~118–134 million years ago (Mya), after Ranunculales diverged with core eudicots at ~123–139 Mya. Moreover, we characterized genomic fractionation resulting from gene loss and retention after polyploidizations. Notably, we revealed a high degree of divergence between subgenomes. In particular, synonymous nucleotide substitutions at synonymous sites (Ks) and phylogenomic analyses implied that A. coerulea might provide the subgenome(s) for the gamma-hexaploid hybridization.
... Microsatellite DNA markers are useful for routine and affordable analysis; however, they do have limitations such as the limited number of loci sampled and the presence of null alleles in some species which may skew the results. Future studies can make use of recently published macadamia genome assemblies (Niu et al. 2020;Nock et al. 2020) to mine more SSR markers across the genome, thereby improving discriminating power of the existing marker panels. A further limitation of our study was not having wild representatives of M. integrifolia and M. tetraphylla to serve as species references; hence, the species composition of the groupings observed is putative and based on records of the accessions they contain. ...
Macadamia nuts are known globally for their high quality and economic value. Global macadamia commercial nut production amounts to 60,000 metric tonnes and is increasing steadily. South Africa is the leading producer with 29% of worldwide kernel production. Commercial macadamia germplasm was originally selected from a small genepool (mainly Macadamia integrifolia species) from a limited geographic distribution in Australia. These accessions were subsequently bred, cloned and exported across the world to start local macadamia industries. The South African macadamia industry was established with pre-commercial and commercial macadamia from different parts of the world, and local selections were also performed. Many of these accessions have unique genetic compositions that have not been characterized yet. We used 13 nuclear microsatellite markers to study the genetic diversity and structure of macadamia germplasm cultivated in South Africa. We compared four groups of accessions including 31 originating from the Hawaiian Agricultural Experimental Station (HAES), 19 from Australia (AUS), two from California and one from Israel (OTH), 31 from South Africa’s locally selected accessions (SA) and 26 from two local Farmers (FARM). We used STRUCTURE, PCoA and neighbour-joining phylogenetic analyses to show that the South African selected accessions include diverse hybrid genotypes with strong Macadamia tetraphylla composition, unlike the Hawaiian commercially released and Australian representative collections that mostly have M. integrifolia or hybrid composition. Our results suggest that the South African selections represent a unique and diverse set of germplasm for future macadamia improvement efforts that will benefit from genomic breeding technologies.
... VIGR provides a reliable high throughput platform to advance both functional genomic studies in non-model horticultural crops producing fruits, vegetables, nuts, or ornamental features. Functional genomics in non-model crops has been expanded through recent advances in de novo assembly of plant genomes, such as pineapple [189], almond [190,191], mango [192], macadamia [193] and avocado [194] where new genomic knowledge can now lead to improved functional annotation. VIGR in combination with phylogenetics, metabolomics, transcriptomics and/or genomic approaches can advance gene characterisation and protein function in non-model species (Fig. 3A). ...
Multipartite viral vectors provide a simple, inexpensive and effective biotechnological tool to transiently manipulate (i.e. reduce or increase) gene expression in planta and characterise the function of genetic traits. The development of virus-induced gene regulation (VIGR) systems usually involve the targeted silencing or overexpression of genes involved in pigment biosynthesis or degradation in plastids, thereby providing rapid visual assessment of success in establishing RNA- or DNA-based VIGR systems in planta. Carotenoids pigments provide plant tissues with an array of yellow, orange, and pinkish-red colours. VIGR-induced transient manipulation of carotenoid-related gene expression has advanced our understanding of carotenoid biosynthesis, regulation, accumulation and degradation, as well as plastid signalling processes. In this review, we describe mechanisms of VIGR, the importance of carotenoids as visual markers of technology development, and knowledge gained through manipulating carotenogenesis in model plants as well as horticultural crops not always amenable to transgenic approaches. We outline how VIGR can be utilised in plants to fast-track the characterisation of gene function(s), accelerate fruit tree breeding programs, edit genomes, and biofortify plant products enriched in carotenoid micronutrients for horticultural innovation.
